Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>&gt;</code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.

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== Prerequisites ==

== Prerequisites ==

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The [https://confluence.slac.stanford.edu/display/PCDS/Data+Management Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''pyana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.

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The [https://confluence.slac.stanford.edu/display/PSDM/Software+Distribution Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''psana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.

Revision as of 09:22, 28 May 2015

Note that throughout the instructions $ denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use % or > for that purpose. The prompt should not be included in the commands typed to the shell.

Prerequisites

The Photon Science Data Management (PSDM) software distribution must be installed. The PSDM software distribution provides psana, which is a critical dependency of cctbx.xfel. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.

Site

Installation root directory

Notes

BNL

/usr/local/crys/psdm

CCI, LBNL

/net/viper/raid1/psdm

Only available on viper.lbl.gov

NERSC

/global/project/projectdirs/lcls/psdm-carver

Only to be used on the carver system

SLAC

/reg/g/psdm

The PSDM software distribution is supported on the most popular flavors of Linux and is installed at several sites worldwide. Separate installation and maintenance instructions are provided by the PSDM project at PSDM software distribution. The package can be installed anywhere on the filesystem, and it is generally possible to install it without superuser privileges.

Create a test release and an analysis package

A test release, which refers to a particular release of the PSDM distribution, is represented by a directory in the file system, often called analysis-rel or myrelease. An analysis package within the test release in turn refers to the files implementing the analysis modules of the package. Details about test releases and analysis packages are covered in Analysis Workbook. Quick Tour. To prepare the environment for using the PSDM software distribution, bash-users should source ana_env.sh,

$ . /path/to/psdm/etc/ana_env.sh

where /path/to/psdm should be replaced with the path to the installation root directory. csh-users should source ana_env.csh instead,

% source /path/to/psdm/etc/ana_env.csh

Sourcing ana_env.sh or ana_env.csh only modifies the environment of the current shell, and would have to be repeated every time a new shell is started. To make the changes persistent, add

to ~/.cshrc as appropriate. This ensures the environment is properly prepared for non-interactive shells, e.g. the shells that are used to run jobs submitted to the cluster. To also be able to use the PSDM software from interactive shells, it is recommended that bash-users put

test -r ~/.bashrc && . ~/.bashrc

near the top of ~/.bash_profile. There is no need to edit any additional files for csh-users, because csh always reads ~/.cshrc.

A test released based on the most current PSDM distribution is then set up in the current working directory using